public class URLScanner
{
...
   protected void handleArchiveByFile(File file, ...) ...
   {
      ...

         ZipFile zip = new ZipFile(file);
         Enumeration<? extends ZipEntry> entries = zip.entries();
         // Replace out the default classloader with one for the zip
         URLClassLoader classLoader = new URLClassLoader(new URL[] { file.toURI().toURL() }); // PROBLEM PART 1: delegates first to parent classloader
         while (entries.hasMoreElements())
         {
            ZipEntry entry = entries.nextElement();
            String name = entry.getName();
            handle(..., classLoader.getResource(name), ...); // PROBLEM PART 2: if parent classloader contains that name, the file content is ignored!
         }
      ...
   }
...
}

file = /tmp/tomcat-embedded-6/work/arquillian-tomcat-embedded-6/localhost/guvnor-webapp-5.3.0-SNAPSHOT/WEB-INF/lib/seam-persistence-api-3.1.0.Beta2.jar
classLoader = URL is file:/tmp/tomcat-embedded-6/work/arquillian-tomcat-embedded-6/localhost/guvnor-webapp-5.3.0-SNAPSHOT/WEB-INF/lib/seam-persistence-api-3.1.0.Beta2.jar
for each entry, when:
  name = "META-INF/beans.xml"
  classLoader.getResource(name) = file:/home/gdesmet/projects/jboss/forked-guvnor/guvnor-webapp/target/classes/META-INF/beans.xml // WRONG
  // Should be = .../seam-persistence-api-3.1.0.Beta2.jar!META-INF/beans.xml

Handle file META-INF/beans.xml from file:/home/gdesmet/projects/jboss/forked-guvnor/guvnor-webapp/target/classes/META-INF/beans.xml
Handle file META-INF/beans.xml from file:/home/gdesmet/projects/jboss/forked-guvnor/guvnor-webapp/target/classes/META-INF/beans.xml
Handle file META-INF/beans.xml from file:/home/gdesmet/projects/jboss/forked-guvnor/guvnor-webapp/target/classes/META-INF/beans.xml
...